Thank you all for your suggestions concerning pair-wise distances. The motivation behind my question is that I am writing a simplistic molecular dynamics program, where hard disks move freely inside a plane region, except when colliding with boudaries or with other disks. I hoped that my program could be as fast as the beautiful Python program of Jake Vanderplas (http://jakevdp.github.com) but, up to now, the Python code is still significantly faster.
JP Grive
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